Over-fertilization has a significant impact on soil microbial properties and its ecological environment. However, the effects of long-term fertilization on microbial properties on a large scale are still vague. This meta-analysis collected 6211 data points from 109 long-term experimental sites in China to evaluate the effects of fertilizer type and fertilization duration, as well as soil and climate conditions, on the effect sizes on various microbial properties and indices. The organic fertilizers combined with straw (NPKS) and manure (NPKM) had the highest effect sizes, while the chemical fertilizers N (sole N fertilizer) and NPK (NPK fertilizer) had the lowest. When compared with the control, NPKM treatment had the highest effect size, while N treatment had the lowest effect size on MBN (111% vs. 19%), PLFA (110% vs. −7%), fungi (88% vs. 43%), Actinomycetes (97% vs. 44%), urease (77% vs. 25%), catalase (15% vs. −11%), and phosphatase (58% vs. 4%). NPKM treatment had the highest while NPK treatment had the lowest effect size on bacteria (123% vs. 33%). NPKS treatment had the highest while N treatment had the lowest effect sizes on MBC (77% vs. 8%) and invertase (59% vs. 0.2%). NPKS treatment had the highest while NPK treatment had the lowest effect size on the Shannon index (5% vs. 1%). The effect sizes of NPKM treatment were the highest predominantly in arid regions because of the naturally low organic carbon in soils of these regions. The effect sizes on various microbial properties were also highly dependent on soil texture. In coarse-textured soils the effect sizes on MBC and MBN peaked sooner compared with those of clayey or silty soils, although various enzymes were most active in silty soils during the first 10 years of fertilization. Effect sizes on microbial properties were generally higher under NPKM and NPKS treatments than under NPK or N treatments, with considerable effects due to climate conditions. The optimal field fertilizer regime could be determined based on the effects of fertilizer type on soil microorganisms under various climate conditions and soil textures. This will contribute to the microbial biodiversity and soil health of agricultural land. Such controls should be used for adaptation of fertilization strategies to global changes.